Hi Carl and thanks for popping back to explain your symptoms in some more detail, great work
I think we have plenty to go on and my run down of the noise goes this way...
Firstly this is exactly the noise I experience from my Fiesta, lots of Fiesta and Ka owners mention similar sounds/noises from their gearbox because Ford used the same gearbox across a variety of models and for a long time. I believe the gearbox design dates back to the OHV 'Kent' engine used in the Fiesta MK1. Anyway..
I don't think the noise is related to the flywheel or clutch assembly. If it were, then the noise would change relative to the engine RPMs, NOT the gear selected (and speed).
The noise is most probably the layshaft or input shaft. Depending on the gear selected, the speed of the layshaft will change according to the input shaft. It's rather complicated, but simply..(Just examples!!)
1st gear - one rotation of the input shaft is 5 rotations of the layshaft
2nd gear - one rotation of the input shaft is 4 rotations of the layshaft
3rd gear - one rotation of the input shaft is 3 rotations of the layshaft
4th gear - one rotation of the input shaft is 2 rotations of the layshaft
5th gear - one rotation of the input shaft is one rotation of the layshaft
So when you're in the lower gears the layshaft is turning faster relative to the input shaft at 20mph than it would in the higher gears. So any noise from the bearings would be a lot more noticable at these speeds and in certain gears.
That's what I think is going on, now you could replace the gearbox but you would probably find the noise is still there, maybe just quieter. It's honestly the design of these gearboxes, if you Google search "Ford Fiesta Gearbox Noise" you'll see what I mean, some people have spent ££££s on new clutches, flywheels and refurbished gearboxes and much to their dissapointment the noise hasn't gone.
The allen key plug you've found is the top up/level plug. Park your car on level ground (very important) and remove this plug. There's a little thin washer, it should be okay to be reused once. Buy the oil which Jamie kindly listed and top up your gearbox oil, keep going until it leaks out - that's when it's at the correct level. You will probably find the noise is quieter and especially when warm you won't hear it at all, but that's down to the viscosity of the oil being slightly thinner when the gearbox heats up.
I have probably made mistakes as it's been a while since I did my NVQ3 and LGV training! But the basic principle is here and nobody's perfect
Best of luck mate!!